Summary Complex interactions between numerous specialized host cells in gut, liver and other locations, polymorphisms of multiple susceptibility genes and their associated signaling pathways and functions, and a myriad of microbial and other environmental factors are emerging as central to the pathogenesis of many of the most important digestive diseases, as exemplified by inflammatory bowel disease (IBD) and non-alcoholic fatty liver disease (NAFLD). It is becomingly increasingly evident that more comprehensive views of the players and interactions are needed to unravel many of the most perplexing digestive diseases. Consequently, tools to characterize and define multiple host and microbial cells and their gene expression responses are increasingly important and essential for digestive diseases research. Most advanced among these tools are technologies based on high- throughput sequencing, as it is now routinely possible to obtain hundreds of millions of base pairs of sequence at modest costs. Next-generation sequencing technologies have revolutionized basic and translational research in medicine over the last several years, and are in increasing demand in digestive diseases research. Consequently, we have designed the Microbiomics and Functional Genomics Core to provide advanced microbiomics and genomics services to Center members, and offer consultation and training in genomics technologies to enhance the ability of members to implement these technologies in their research. Specifically, the Core will: 1) Conduct sequencing-based assays for microbiomics and functional genomics; 2) Perform bioinformatics analyses of sequencing-based assays; 3) Consult and advise in studies involving microbiomics and functional genomics; and 4) Provide validated experimental protocols and training. The Core leverages several established institutional shared resources, including the Center for Microbiome Innovation at the University of California, San Diego (UCSD), the Genomics Center of the Institute for Genomic Medicine at UCSD, and the UCSD Center for Computational Biology and Bioinformatics. This unique combination and integration of outstanding existing resources will ensure that Center members have access to cutting-edge technologies for studies involving microbiomics and functional genomics. The Core will be directed by internationally recognized experts in microbiomics (Dr. Rob Knight) and functional genomics (Dr. Christopher Glass), and other Core personnel are highly experienced in microbiome science, molecular genetics, bioinformatics and computational biology. The Core has established rigorous procedures for quality control and data validation. Together, this infrastructure and expertise will enable the Microbiomics and Functional Genomics Core to provide a range of high quality and cost-effective microbiomics and functional genomics services that greatly enhance the ability of Center members to advance digestive diseases research.